Abstract
High salinity is a major abiotic stressor that affects crop productivity and quality. While proper seedling growth is critical for crop reproduction under high salinity stress. Nowadays, genes/miRNAs expression is used for studying salinity stress response in rice seedlings. However, analysis of miRNA combined with gene expression is rare. To this end, we used miRNA-seq and gene expression profile to ascertain 6335 genes (3276 genes up-regulated, 3059 genes down-regulated) and 126 miRNAs (47 miRNAs up-regulated, 79 miRNAs down-regulated) that respond to salinity stress in rice seedlings. We then used these 126 miRNAs (including the novel miRNA osa-Chr12_1506) to identify 121 differentially expressed predicted target genes. In addition, we identified 34 miRNA-target RNA pairs, consisting of 9 differentially expressed miRNAs with complementary expression patterns. Combined with previous studies, we proposed a simple model for the molecular mechanism of a 12-h salinity stress response in rice seedlings. The findings lead to a deeper understanding of the function of miRNAs and genes that respond to salinity, and contributed to the elucidation of the complex mechanisms activated by salinity stress.
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Acknowledgements
This research was supported by the National Science Fund of China (nos. 31070276 and 31270360). We would like to thank Guang Zhou Gene Denonvo Bio-tech for supporting the analysis of partial data.
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Raw reads of the transcriptome have been deposited into the NCBI Short Read Archive (SRA, http://www.ncbi.nlm.nih.gov/sra/) under the accession numbers: SRR2886945, SRR2786811, SRR2890846 and SRR2890862.
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Communicated by Y. Wang.
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11738_2017_2570_MOESM4_ESM.xlsx
Supplementary material 4 (XLSX 11 kb) Table S1: The statistics of Solexa Sequencing and the mapping results of miRNA-seq reads
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Supplementary material 5 (XLSX 10 kb) Table S2: Specific primers information for qRT-PCR and miRNAs for stem-loop RT-PCR
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Supplementary material 7 (XLSX 24 kb) Table S4: miRNAs and their target genes respond to salinity stress in rice seedlings
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Wang, Q., Geng, T., Zhu, S. et al. Analysis of miRNA-seq combined with gene expression profile reveals the complexity of salinity stress response in Oryza sativa . Acta Physiol Plant 39, 272 (2017). https://doi.org/10.1007/s11738-017-2570-y
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DOI: https://doi.org/10.1007/s11738-017-2570-y